The present invention provides a method for determining low mass ions for diagnosing colorectal cancer by using a MALDI-TOF mass spectrometer to biostatistically analyze low mass ions, which are extracted from a biological sample, and a method for providing information for diagnosing colorectal cancer using same. The present inventions can provide a diagnostic method, which requires low cost and a short time for analysis, can analyze large areas, and which can provide superior and credible discriminations.
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1. A method for determining low mass ions for diagnosing colorectal cancer (CRC) in a mammal, the method comprising steps of: (a) taking low mass ion mass spectra from a plurality of biological samples of a plurality of mammals wherein the biological samples being prepared by a chemical extracting step, using a mass spectrometer and extracting peak intensities of low mass ions from the low mass ion mass spectra; (b) performing a biostatistical analysis on the acquired peak intensities to calculate a discriminant score (DS) for each peak; (c) primarily selecting peaks of the respective cases from among the peaks, in which the primarily selected peaks meet a condition that an absolute value of a product of the peak intensities multiplied by factor loadings of the respective peaks exceeds T 1 ; (d) secondarily selecting peaks from the primarily selected peaks for the respective cases, in which the secondarily selected peaks are commonly present in the cases which are T 2 or greater percent of the training set cases; and (e) determining a group of low mass ions for diagnosing CRC with the peaks selected at the step (d) wherein after the step (d), the discriminant score (DS) is calculated only with the peaks selected at the step (d) so that sensitivity and specificity are calculated according to the calculated DS, and if the calculated sensitivity is less than N 3 or if the calculated specificity is less than N 4 , the T 1 and T 2 are changed so that the steps (c) and (d).
A method for identifying low mass ions to diagnose colorectal cancer (CRC) in mammals. The process involves: (a) Obtaining mass spectra of low mass ions from multiple biological samples from different mammals, preparing the samples using chemical extraction, analyzing with a mass spectrometer, and recording peak intensities of the low mass ions; (b) Applying biostatistical analysis to the peak intensities to compute a discriminant score (DS) for each peak; (c) Initially selecting peaks where the absolute value of (peak intensity * factor loading) exceeds a threshold T1; (d) Further narrowing the selection to peaks commonly found in at least T2 percent of the training set cases; (e) Determining a group of low mass ions for diagnosing CRC using the peaks selected in step (d). After step (d), the discriminant score (DS) is recalculated using only the selected peaks to calculate sensitivity and specificity. T1 and T2 are adjusted iteratively if the calculated sensitivity is less than N3, or if the calculated specificity is less than N4.
2. The method as set forth in claim 1 , wherein the step (d) comprises a step (d1) of primarily selecting peaks of the respective cases from among the peaks, in which the primarily selected peaks meet a condition that an absolute value of a product of the peak intensities multiplied by factor loadings of the respective peaks exceeds T 1 .
The method for identifying low mass ions to diagnose colorectal cancer (CRC) as previously described, specifically where the step of secondarily selecting peaks (d) includes primarily selecting peaks of the respective cases from among the peaks, in which the primarily selected peaks meet a condition that an absolute value of a product of the peak intensities multiplied by factor loadings of the respective peaks exceeds T 1.
3. The method as set forth in claim 1 , wherein the step (d) further comprises a step (d1) of selecting predetermined peaks from among the peaks selected at the step (d) to calculate DS for validation set cases, calculating sensitivity and specificity according to the calculated DS, and if the calculated sensitivity is less than N 5 or if the calculated specificity is less than N 6 , re-selecting new peaks that are different from the predetermined peaks and reiterating a process of improving discrimination performance with respect to validation set cases and finally selecting mass value of the low mass ions for diagnosing CRC.
The method for identifying low mass ions to diagnose colorectal cancer (CRC) as previously described, further comprising a validation step in selecting peaks (d). Predetermined peaks from those previously selected are used to calculate a DS for validation set cases. Sensitivity and specificity are calculated based on this DS. If sensitivity is below N5 or specificity is below N6, different peaks are re-selected, and the process of improving discrimination performance is repeated until suitable low mass ions for CRC diagnosis are identified.
4. The method as set forth in claim 3 , wherein the low mass ions for diagnosing CRC comprise low mass ions of fibrinogen or fibrinogen alpha chain.
The method for identifying low mass ions to diagnose colorectal cancer (CRC) using an iterative validation process, where the low mass ions identified for diagnosing CRC include low mass ions derived from fibrinogen or fibrinogen alpha chain.
5. The method as set forth in claim 3 , wherein the low mass ions for diagnosing CRC comprises low mass ions of phosphoenolpyruvate (PEP).
The method for identifying low mass ions to diagnose colorectal cancer (CRC) using an iterative validation process, where the low mass ions identified for diagnosing CRC include low mass ions derived from phosphoenolpyruvate (PEP).
6. The method as set forth in claim 1 , wherein the step (c) comprises: a step (c1) of calculating sensitivity and specificity according to the calculated DS; a step (c2) of excluding false positive or false negative cases from the plurality of cases, if the sensitivity is less than N 1 or if the specificity is less than N 2 , and reiterating the steps (a) to (b); and a step (c3) of selecting the cases as the predetermined training set cases if the sensitivity is equal to or greater than N 1 and if the specificity is equal to or greater than N 2 .
The method for identifying low mass ions to diagnose colorectal cancer (CRC) as previously described, where the initial peak selection (c) involves: (c1) Calculating sensitivity and specificity using the discriminant score (DS); (c2) If sensitivity is below N1 or specificity is below N2, excluding false positive or false negative cases and repeating steps (a) and (b); and (c3) Designating cases as the predetermined training set if sensitivity is at least N1 and specificity is at least N2.
7. The method as set forth in claim 1 , wherein the step (a) comprises a step (a1) of aligning low mass ion mass spectra acquired from the biological samples of the plurality of cases and importing.
The method for identifying low mass ions to diagnose colorectal cancer (CRC) as previously described, where the initial data acquisition (a) includes aligning and importing low mass ion mass spectra acquired from biological samples from the different mammals.
8. The method as set forth in claim 1 , wherein the step (b) comprises: a step (b1) of normalizing the imported peak intensities; a step (b2) of scaling the normalized peak intensities; and a step (b3) of calculating the DS by performing a biostatistical analysis on the scaled peak intensities.
The method for identifying low mass ions to diagnose colorectal cancer (CRC) as previously described, where the biostatistical analysis (b) involves: (b1) Normalizing the imported peak intensities; (b2) Scaling the normalized peak intensities; and (b3) Calculating the discriminant score (DS) by performing biostatistical analysis on the scaled peak intensities.
9. The method as set forth in claim 8 , wherein the scaling is a Pareto scaling.
The method for identifying low mass ions to diagnose colorectal cancer (CRC) involving normalization, scaling, and biostatistical analysis, where the scaling method used is Pareto scaling.
10. The method as set forth in claim 8 , wherein the biostatsitical analysis is a principal component analysis-based linear discriminant analysis (PCA-DA).
The method for identifying low mass ions to diagnose colorectal cancer (CRC) involving normalization, scaling, and biostatistical analysis, where the biostatistical analysis used is a principal component analysis-based linear discriminant analysis (PCA-DA).
11. The method of claim 1 , wherein the peak intensities of low mass ions are extracted and the biostatistical analysis is performed with software in a computer.
The method for identifying low mass ions to diagnose colorectal cancer (CRC), where the extraction of peak intensities and the biostatistical analysis are performed using software on a computer.
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August 12, 2011
May 2, 2017
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